buildH
Build hydrogens from a united-atom MD of lipids and calculate the order parameter.
Features
BuildH can :
- reconstruct hydrogens from a united-atom structure file (PDB, GRO) or a trajectory.
- calculate the order parameter based on the reconstructed hydrogens
- write a new structure/trajectory file with the reconstructed hydrogens
BuildH works in two modes :
- A slow mode when an output trajectory (e.g. in xtc format) is requested by the user. In this case, the whole trajectory including newly built hydrogens are written to this trajectory.
- A fast mode without any output trajectory.
Requirements
Python >= 3.6 is mandatory for running buildH.
buildH is written in Python 3 and need the following modules :
- numpy
- pandas
- MDAnalysis.
This is automatically taken into account if you follow the procedure below.
Installation (development)
-
Install conda (either with Miniconda or Anaconda, we recommend Miniconda)
-
Clone this GitHub repository:
$ git clone https://github.com/patrickfuchs/buildH.git
$ cd buildH
- Create conda environment:
$ conda env create -f binder/environment.yml
$ conda activate buildh
If needed, update your conda env with
$ conda env update -f binder/environment.yml
- Install the dev version of buildH:
$ pip install -e .
Usage
$ buildH
usage: buildH [-h] -c COORD [-t TRAJ] -l LIPID [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]]
-d DEFOP [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-pi PICKLE]
This program builds hydrogens and calculate the order parameters (OP) from a
united-atom trajectory. If -opx is requested, pdb and xtc output files with
hydrogens are created but OP calculation will be slow. If no trajectory output
is requested (no use of flag -opx), it uses a fast procedure to build
hydrogens and calculate the OP.
optional arguments:
-h, --help show this help message and exit
-c COORD, --coord COORD
Coordinate file (pdb or gro).
-t TRAJ, --traj TRAJ Input trajectory file. Could be in XTC, TRR or DCD format.
-l LIPID, --lipid LIPID
Residue name of lipid to calculate the OP on (e.g.
POPC).
-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...], --lipid_topology LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]
User topology lipid json file(s). Mandatory to build hydrogens.
-d DEFOP, --defop DEFOP
Order parameter definition file. Can be found on
NMRlipids MATCH repository:https://github.com/NMRLipid
s/MATCH/tree/master/scripts/orderParm_defs
-opx OPDBXTC, --opdbxtc OPDBXTC
Base name for trajectory output with hydrogens. File
extension will be automatically added. For example
-opx trajH will generate trajH.pdb and trajH.xtc. So
far only xtc is supported.
-o OUT, --out OUT Output base name for storing order parameters.
Extention ".out" will be automatically added. Default
name is OP_buildH.out.
-b BEGIN, --begin BEGIN
The first frame (ps) to read from the trajectory.
-e END, --end END The last frame (ps) to read from the trajectory.
-pi PICKLE, --pickle PICKLE
Output pickle filename. The structure pickled is a dictonnary containing for each Order parameter,
the value of each lipid and each frame as a matric
The list of supported lipids (-l option) are: CHARMM_POPC, Berger_POPC, Berger_PLA, Berger_POP.
The program needs one mandatory file (present in this repo):
order_parameter_definitions_MODEL_Berger_POPC.def
(option-d
).
Further documentation
Some more documentation can be found in the directory docs
:
- Explanation of the different file formats.
- Examples of how to launch buildH.
- Validation of buildH.
- The geometric algorithm on how H are rebuilt.
Contributors
- Patrick Fuchs
- Amélie Bacle
- Hubert Santuz
- Pierre Poulain
Licence
buildH is licensed under the BSD License.